Difference between revisions of "FALCON"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
|||
| Line 26: | Line 26: | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
Revision as of 13:37, 13 June 2022
Description
Falcon: a set of tools for fast aligning long reads for consensus and assembly
The Falcon tool kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience.
We use FALCON-integrate in conjunction with SLURM to run FALCON on HiPerGator. See the sample SLURM fc_run.cfg for an example. For a larger run consider modifying DAligner options to set a memory limit on kmer search with -M. See sample SLURM fc_large_run.cfg for an example.
Environment Modules
Run module spider falcon to find out what environment modules are available for this application.
System Variables
- HPC_FALCON_DIR - installation directory
Additional Information
Errors and Pitfalls
- Make sure that the fasta headers are in a format acceptable to FALCON. If you encounterd a Fasta2DB error '
Line 1: Pacbio header line format error' see FALCON issue #251 for an explanation.
- TAP is a part of FALCON module.